rs17475512

Variant names:

• chr7-102872041-A-G
• rs17475512
• NM_001394494.2:c.1905+5426T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394494.2(FBXL13):​c.1905+5426T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 152,168 control chromosomes in the GnomAD database, including 576 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.073 (576 hom., cov: 32)
• Consequence: FBXL13 NM_001394494.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 7 publications found

Genes affected

FBXL13 (HGNC:21658): (F-box and leucine rich repeat protein 13) Members of the F-box protein family, such as FBXL13, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (MIM 601434), cullin (see CUL1; MIM 603134), and F-box proteins, act as protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains (Jin et al., 2004 [PubMed 15520277]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394494.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBXL13	NM_001394494.2	MANE Select	c.1905+5426T>C		intron	N/A	NP_001381423.1	C9JI88
	FBXL13	NM_145032.3		c.1635+5426T>C		intron	N/A	NP_659469.3	Q8N1P0
	FBXL13	NM_001287150.2		c.1635+5426T>C		intron	N/A	NP_001274079.1	Q8NEE6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBXL13	ENST00000440067.4	TSL:3 MANE Select	c.1905+5426T>C		intron	N/A	ENSP00000390126.2	C9JI88
	FBXL13	ENST00000379305.7	TSL:1	n.*1634+5426T>C		intron	N/A	ENSP00000368607.4	A0A8V8NC12
	FBXL13	ENST00000448002.6	TSL:1	n.1905+5426T>C		intron	N/A	ENSP00000405434.2	E7ERH8

Frequencies

GnomAD3 genomes AF: 0.0728 AC: 11073 AN: 152050 Hom.: 575 Cov.: 32

Gnomad AFR AF: 0.0206

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0232

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0942

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0727 AC: 11070 AN: 152168 Hom.: 576 Cov.: 32 AF XY: 0.0704 AC XY: 5235 AN XY: 74386

African (AFR) AF: 0.0205 AC: 852 AN: 41528

American (AMR) AF: 0.0873 AC: 1334 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0232 AC: 112 AN: 4820

European-Finnish (FIN) AF: 0.0870 AC: 922 AN: 10594

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.106 AC: 7222 AN: 67990

Other (OTH) AF: 0.0932 AC: 197 AN: 2114

Alfa AF: 0.0793 Hom.: 560

Bravo AF: 0.0731

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.50
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17475512; hg19: chr7-102512488;